2024-07-24

Shiny Server and OpenCPU Server for Dimensional Reduction Applications with an scRNAseq Bioinformatics Pipeline

Outline

  • Project Recap

  • Accomplishments

  • Challenges

  • Next Week’s to-do

Project Recap

1. Develop and implement a bioinformatics pipeline

  • Deploy RStudio, Shiny, and OpenCPU servers using Docker
    • Easy development and access: Access of the servers via a browser using docker
    • From git, isolated and standalone applications can be started via Docker
  1. Expose a stateless microservice using RESTful API and RPC the major steps in scRNAseq pipeline and their visualizations
  2. Develop an interactive dashboard/reactive framework in Shiny for the scRNA pre-processing pipeline

Current Progress

Successful trial runs

Deployed trial shiny package

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Shiny applications not supported in static R Markdown documents

Challenges

  • Deploy the servers using Docker
    • Containers for the trial package are on private and yet to establish a host connection
  • To improve and polish scripts for future deployment

Next week’s to-do

  • Attend lectures
  • Test run main pipeline for pre-processing of scRNA using Seurat package
  • Deploy the step/s of the pipeline using Docker